sc.fiji.snt

Class SNTService

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

org.scijava.service.AbstractService

sc.fiji.snt.SNTService

All Implemented Interfaces:

java.lang.Comparable<org.scijava.Prioritized>, net.imagej.ImageJService, org.scijava.Contextual, org.scijava.Disposable, org.scijava.Identifiable, org.scijava.Initializable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.service.Service, org.scijava.Versioned

public class SNTService
extends org.scijava.service.AbstractService
implements net.imagej.ImageJService

Service for accessing and scripting the active instance of SNT.

Author:

Tiago Ferreira, Kyle Harrington

Constructor Summary

Constructors

Constructor and Description
SNTService()

Method Summary

Modifier and Type	Method and Description
void	assignValues(boolean selectedPathsOnly) Assigns pixel intensities at each Path node, storing them as Path values.
ij.ImagePlus	captureView(java.lang.String view, boolean project) Retrieves a WYSIWYG 'snapshot' of a tracing canvas.
Tree	demoTree() Returns a toy reconstruction (fractal tree).
ij.ImagePlus	demoTreeImage() Returns the image associated with the demo (fractal) tree.
java.util.List<Tree>	demoTrees() Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database).
void	dispose() Quits SNT.
TreeAnalyzer	getAnalyzer(boolean selectedPathsOnly) Returns a TreeAnalyzer instance constructed from current Paths.
SciViewSNT	getOrCreateSciViewSNT()
PathAndFillManager	getPathAndFillManager() Returns the PathAndFillManager associated with the current SNT instance.
java.util.List<Path>	getPaths() Gets the paths currently listed in the Path Manager
SNT	getPlugin() Returns a reference to the active SNT plugin.
Viewer3D	getRecViewer() Returns a reference to SNT's Reconstruction Viewer.
Viewer3D	getRecViewer(int id) Returns a reference to an opened Reconstruction Viewer (standalone instance).
SciViewSNT	getSciViewSNT()
java.util.Collection<Path>	getSelectedPaths() Gets the paths currently selected in the Path Manager list.
TreeStatistics	getStatistics(boolean selectedPathsOnly) Returns a TreeStatistics instance constructed from current Paths.
org.scijava.table.DefaultGenericTable	getTable() Returns a reference to SNT's main table of measurements.
Tree	getTree(boolean selectedPathsOnly) Gets the collection of paths listed in the Path Manager as a Tree object.
SNTUI	getUI() Returns a reference to SNT's UI.
SNT	initialize(boolean startUI) Initializes SNT.
SNT	initialize(ij.ImagePlus imp, boolean startUI) Initializes SNT.
SNT	initialize(java.lang.String imagePath, boolean startUI) Initializes SNT.
boolean	isActive() Gets whether SNT is running.
void	loadTracings(java.lang.String filePath) Loads the specified tracings file.
void	loadTree(Tree tree) Loads the specified tree.
Viewer3D	newRecViewer(boolean guiControls) Instantiates a new standalone Reconstruction Viewer.
boolean	save(java.lang.String filePath) Saves all the existing paths to a file.
void	updateViewers() Script-friendly method for updating (refreshing) all viewers currently in use by SNT.

Methods inherited from class org.scijava.service.AbstractService

getContext, setContext, toString

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority

Methods inherited from class org.scijava.AbstractContextual

context

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.scijava.service.Service

initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier, log

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Versioned

getVersion

Constructor Detail

SNTService

public SNTService()

Method Detail

isActive

public boolean isActive()

Gets whether SNT is running.

Returns:

true if this SNTService is active, tied to the active instance of SNT

assignValues

public void assignValues(boolean selectedPathsOnly)
                  throws java.lang.UnsupportedOperationException,
                         java.lang.IllegalArgumentException

Assigns pixel intensities at each Path node, storing them as Path values. Assigned intensities are those of the channel and time point currently being traced. Assumes SNT has been initialized with a valid image.

Parameters:

selectedPathsOnly - If true, only selected paths will be assigned values, otherwise voxel intensities will be assigned to all paths

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

java.lang.IllegalArgumentException - If valid imaged data is not available

See Also:

PathProfiler, Path.setNodeValues(double[])

initialize

public SNT initialize(boolean startUI)

Initializes SNT. Since no image is specified, tracing functions are disabled.

Parameters:

startUI - Whether SNT's UI should also be initialized;

Returns:

the SNT instance.

initialize

public SNT initialize(java.lang.String imagePath,
                      boolean startUI)

Initializes SNT.

Parameters:

imagePath - the image to be traced. If "demo" (case insensitive), SNT is initialized using the demoTreeImage(). If empty or null and SNT's UI is available an "Open" dialog prompt is displayed.

startUI - Whether SNT's UI should also be initialized;

Returns:

the SNT instance.

initialize

public SNT initialize(ij.ImagePlus imp,
                      boolean startUI)

Initializes SNT.

Parameters:

imp - the image to be traced (null not allowed)

startUI - Whether SNT's UI should also be initialized;

Returns:

the SNT instance.

getPlugin

public SNT getPlugin()

Returns a reference to the active SNT plugin.

Returns:

the SNT instance

loadTracings

public void loadTracings(java.lang.String filePath)

Loads the specified tracings file.

Parameters:

filePath - either a "SWC", "TRACES" or "JSON" file. Null not allowed.

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

loadTree

public void loadTree(Tree tree)

Loads the specified tree.

Parameters:

tree - the Tree to be loaded (null not allowed)

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

save

public boolean save(java.lang.String filePath)

Saves all the existing paths to a file.

Parameters:

filePath - the saving output file path. If filePath ends in ".swc" (case insensitive), an SWC file is created, otherwise a "traces" file is created. If empty and a GUI exists, a save prompt is displayed.

Returns:

true, if paths exist and file was successfully written.

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

getSelectedPaths

public java.util.Collection<Path> getSelectedPaths()

Gets the paths currently selected in the Path Manager list.

Returns:

the paths currently selected, or null if no selection exists

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

See Also:

getTree(boolean)

getPaths

public java.util.List<Path> getPaths()

Gets the paths currently listed in the Path Manager

Returns:

all the listed paths, or null if the Path Manager is empty

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

See Also:

getTree(boolean)

getTree

public Tree getTree(boolean selectedPathsOnly)

Gets the collection of paths listed in the Path Manager as a Tree object.

Parameters:

selectedPathsOnly - If true, only selected paths are retrieved

Returns:

the Tree holding the Path collection

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

getAnalyzer

public TreeAnalyzer getAnalyzer(boolean selectedPathsOnly)

Returns a TreeAnalyzer instance constructed from current Paths.

Parameters:

selectedPathsOnly - If true only selected paths will be considered

Returns:

the TreeAnalyzer instance

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

getStatistics

public TreeStatistics getStatistics(boolean selectedPathsOnly)

Returns a TreeStatistics instance constructed from current Paths.

Parameters:

selectedPathsOnly - If true only selected paths will be considered

Returns:

the TreeStatistics instance

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

getPathAndFillManager

public PathAndFillManager getPathAndFillManager()

Returns the PathAndFillManager associated with the current SNT instance.

Returns:

the PathAndFillManager instance

Throws:

java.lang.UnsupportedOperationException - if no SNT instance exists.

updateViewers

public void updateViewers()

Script-friendly method for updating (refreshing) all viewers currently in use by SNT. Does nothing if no SNT instance exists.

getUI

public SNTUI getUI()

Returns a reference to SNT's UI.

Returns:

the SNTUI window, or null if SNT is not running, or is running without GUI

getRecViewer

public Viewer3D getRecViewer()

Returns a reference to SNT's Reconstruction Viewer.

Returns:

SNT's Viewer3D instance.

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

getRecViewer

public Viewer3D getRecViewer(int id)

Returns a reference to an opened Reconstruction Viewer (standalone instance). *

Parameters:

id - the unique numeric ID of the Reconstruction Viewer to be retrieved (as used by the "Script This Viewer" command, and typically displayed in the Viewer's window title)

Returns:

The standalone Viewer3D instance, or null if id was not recognized

newRecViewer

public Viewer3D newRecViewer(boolean guiControls)

Instantiates a new standalone Reconstruction Viewer.

Returns:

The standalone Viewer3D instance

getOrCreateSciViewSNT

public SciViewSNT getOrCreateSciViewSNT()

getSciViewSNT

public SciViewSNT getSciViewSNT()

getTable

public org.scijava.table.DefaultGenericTable getTable()

Returns a reference to SNT's main table of measurements.

Returns:

SNT measurements table

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

demoTree

public Tree demoTree()

Returns a toy reconstruction (fractal tree).

Returns:

a reference to the loaded tree, or null if data could no be retrieved

See Also:

demoTreeImage()

demoTreeImage

public ij.ImagePlus demoTreeImage()

Returns the image associated with the demo (fractal) tree.

Returns:

a reference to the image tree, or null if data could no be retrieved

See Also:

demoTree()

demoTrees

public java.util.List<Tree> demoTrees()

Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database). NB: Data is cached locally. No internet connection required.

Returns:

the list of Trees, corresponding to the dendritic arbors of cells "AA0001", "AA0002", "AA0003", "AA0004" (MouseLight database IDs).

captureView

public ij.ImagePlus captureView(java.lang.String view,
                                boolean project)

Retrieves a WYSIWYG 'snapshot' of a tracing canvas.

Parameters:

view - A case-insensitive string specifying the canvas to be captured. Either "xy" (or "main"), "xz", "zy" or "3d" (for legacy's 3D Viewer).

project - whether the snapshot of 3D image stacks should include its projection (MIP), or just the current plane

Returns:

the snapshot capture of the canvas as an RGB image

Throws:

java.lang.UnsupportedOperationException - if SNT is not running

java.lang.IllegalArgumentException - if view is not a recognized option

dispose

public void dispose()

Quits SNT. Does nothing if SNT is currently not running.

Specified by:

dispose in interface org.scijava.Disposable